gtfparse
Parsing tools for GTF (gene transfer format) files.
Example usage
Parsing all rows of a GTF file into a Pandas DataFrame
from gtfparse import read_gtf
# returns GTF with essential columns such as "feature", "seqname", "start", "end"
# alongside the names of any optional keys which appeared in the attribute column
df = read_gtf("gene_annotations.gtf")
# filter DataFrame to gene entries on chrY
df_genes = df[df["feature"] == "gene"]
df_genes_chrY = df_genes[df_genes["seqname"] == "Y"]Getting gene FPKM values from a StringTie GTF file
from gtfparse import read_gtf
df = read_gtf(
"Transcripts.gtf",
column_converters={"FPKM": float})
gene_fpkms = {
gene_name: fpkm
for (gene_name, fpkm, feature)
in zip(df["seqname"], df["FPKM"], df["feature"])
if feature == "gene"
}